Two comments, on further reading... I love the take on the Witch Character, they have to be lawful, but dont really cast magic, instead they bargain with the dark powers and get an evil imp who allows them to cast spells and who tries to tempt them to become evil. The imp is GM controlled. So there is a pretty good reason the Commonwealthers dont like or trust them.
Is the Witch's Imp mechanic anything like the old Sha'ir (sp?) and their
jen from the 2nd Ed. AD&D "Al-Qadim" Arabian Adventures setting? That was an interesting take on the 'supernatural ally' style of magic I wouldn't mind reviving in a contemporary d20 Past game.
Also Guns are underpowered, sure they are supposed to be on par with 1660's firearms, but if my guns gonna take 4 rounds to reload I want it to hit harder misfire less and be affected by fewer spells.
The 2nd Ed. "Mighty Fortress" Historical Sourcebook had some fixes that dealt with this. Basically gunpowder weapons ignored the first few armour classes at close range (leather was useless at medium ranges, chainmail at short IIRC) and allowed open-ended damage roll-ons. It was historically accurate in some respects - a buff coat, even a steel breastplate were largely useless against the 15mm musketballs that were common in the 17th c.
These mods were used to counteract the effective one-shot nature of 16th-17th c. gunpowder weapons in combat without allowing them to fire at an unrealistically fast rate. It also prevented the introduction of anachronistic revolvers or percussion cap rifles into a 'musketeer and pirate' setting.
The commonality of guns means that quite a few mages have developed low level spells to cause guns to misfire, not fire, or explode. Granted guns can be magically enhanced, but still.
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Regarding masic and gunpowder weaponry. I suppose that if magical affects can be enchanted onto guns (they use the crossbow enchantment costs in D&D3.5 IIRC) minor contingent protection spells could be ensorcelled onto the lock or barrel as well. You know "Protection from Dampness" on the firing-pan, etc.
D&D-style high-power magic would be able to cause effects like soaking a firing pan or prematurely sparking a volatile like gunpowder without too much difficulty. To make the weapons useful counter-spells would doubtless be rapidly devised, based either on counter-spelling or blanket dispelling/negation techniques.
That's notwithstanding wizardly ideological politics regarding such alchemically-derived power as gunpowder in the hands of uninitiated mundanes. Interesting dirty-tricks opportunities present themselves...
